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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ), 'gf_id' => 'HOM05D001106', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001106' ), 'data_identifier' => 'HOM05D001106', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001106', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '553', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02460' => 'bna', 'A02p15110' => 'bna', 'A03p06580' => 'bna', 'A05p20790' => 'bna', 'A07p12630' => 'bna', 'A07p31990' => 'bna', 'A08p26980' => 'bna', 'A09p39380' => 'bna', 'A10p05590' => 'bna', 'A10p24150' => 'bna', 'Aa31LG10G4850' => 'aar', 'Aa31LG11G15160' => 'aar', 'Aa31LG1G8100' => 'aar', 'Aa31LG7G9060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3663' => 'aag', 'Actinidia05958' => 'ach', 'Actinidia14889' => 'ach', 'Actinidia16651' => 'ach', 'Actinidia18936' => 'ach', 'Actinidia23864' => 'ach', 'Actinidia25401' => 'ach', 'Actinidia35086' => 'ach', 'Actinidia36145' => 'ach', 'Ah.08g215180' => 'amhyb', 'Ah.14g084010' => 'amhyb', 'AL1G17160' => 'aly', 'AL1G39860' => 'aly', 'AL1G55990' => 'aly', 'AL2G27420' => 'aly', 'AL2G33690' => 'aly', 'AL6G25080' => 'aly', 'Aqoxy1G01304' => 'aox', 'Aqoxy3G00303' => 'aox', 'Aqoxy3G01341' => 'aox', 'Aqoxy3G01342' => 'aox', 'arahy.Tifrunner.gnm1.ann1.857KFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8MV22J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY8I6Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCSG49' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QP34EV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WEZ503' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVH2H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5M96P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XNQT3T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZUL46H' => 'arhy', 'AT1G07050' => 'ath', 'AT1G25440' => 'ath', 'AT1G49130' => 'ath', 'AT1G68520' => 'ath', 'AT1G73870' => 'ath', 'AT5G14370' => 'ath', 'ATR0824G096' => 'atr', 'ATR1133G053' => 'atr', 'Atru.chr11.64' => 'acertr', 'Atru.chr11.65' => 'acertr', 'Atru.chr3.4135' => 'acertr', 'Atru.chr6.2462' => 'acertr', 'Atru.chr6.2463' => 'acertr', 'Atru.chr9.837' => 'acertr', 'AUR62002867' => 'cqu', 'AUR62030486' => 'cqu', 'AUR62030805' => 'cqu', 'AUR62035221' => 'cqu', 'BcaB01g05115' => 'bca', 'BcaB01g06328' => 'bca', 'BcaB01g06329' => 'bca', 'BcaB01g06376' => 'bca', 'BcaB02g11299' => 'bca', 'BcaB03g12021' => 'bca', 'BcaB03g12022' => 'bca', 'BcaB03g13409' => 'bca', 'BcaB03g13410' => 'bca', 'BcaB03g14046' => 'bca', 'BcaB03g15422' => 'bca', 'BcaB04g17363' => 'bca', 'BcaB05g24391' => 'bca', 'BcaB08g36992' => 'bca', 'BcaC01g01695' => 'bca', 'BcaC03g13495' => 'bca', 'BcaC03g14961' => 'bca', 'BcaC04g19037' => 'bca', 'BcaC05g24669' => 'bca', 'BcaC05g24673' => 'bca', 'BcaC05g26460' => 'bca', 'BcaC05g26666' => 'bca', 'BcaC05g27534' => 'bca', 'BcaC06g35200' => 'bca', 'BcaC06g35201' => 'bca', 'BcaC06g35210' => 'bca', 'BcaC08g45968' => 'bca', 'BcaNung03162' => 'bca', 'BcaNung06762' => 'bca', 'BcaNung06766' => 'bca', 'BolC2t06616H' => 'bol', 'BolC2t08572H' => 'bol', 'BolC3t13261H' => 'bol', 'BolC3t19591H' => 'bol', 'BolC5t29285H' => 'bol', 'BolC5t31235H' => 'bol', 'BolC5t32234H' => 'bol', 'BolC6t38861H' => 'bol', 'BolC7t42374H' => 'bol', 'BolC7t42383H' => 'bol', 'BolC8t47075H' => 'bol', 'BolC8t47430H' => 'bol', 'BolC8t47450H' => 'bol', 'BolC9t59116H' => 'bol', 'BraA02t05216Z' => 'bra', 'BraA02t06577Z' => 'bra', 'BraA03t09990Z' => 'bra', 'BraA05t20985Z' => 'bra', 'BraA07t29041Z' => 'bra', 'BraA07t30829Z' => 'bra', 'BraA08t34644Z' => 'bra', 'BraA09t39442Z' => 'bra', 'BraA10t42820Z' => 'bra', 'BraA10t44479Z' => 'bra', 'C02p06720' => 'bna', 'C02p24810' => 'bna', 'C03p07600' => 'bna', 'C03p72920' => 'bna', 'C05p25030' => 'bna', 'C05p35190' => 'bna', 'C06p37580' => 'bna', 'C07p18630' => 'bna', 'C07p18730' => 'bna', 'C08p05770' => 'bna', 'C09p62790' => 'bna', 'CAN.G438.137' => 'can', 'CAN.G473.39' => 'can', 'CAN.G610.87' => 'can', 'CANSAT01G3252' => 'cansat', 'CANSAT54G0375' => 'cansat', 'CANSAT64G1585' => 'cansat', 'CANSAT80G0543' => 'cansat', 'CANSAT80G0980' => 'cansat', 'CARHR006740' => 'chi', 'CARHR026020' => 'chi', 'CARHR039110' => 'chi', 'CARHR061300' => 'chi', 'CARHR066970' => 'chi', 'CARHR198950' => 'chi', 'Carub.0001s0634' => 'cru', 'Carub.0001s2505' => 'cru', 'Carub.0001s3829' => 'cru', 'Carub.0002s1503' => 'cru', 'Carub.0002s2063' => 'cru', 'Carub.0006s1255' => 'cru', 'Ca_05643_v3' => 'car', 'Ca_11174_v3' => 'car', 'Ca_13833_v3' => 'car', 'Ca_25449_v3' => 'car', 'CBR_g51017' => 'cbr', 'Cc01_g14750' => 'ccan', 'Cc04_g07160' => 'ccan', 'Cc07_g00200' => 'ccan', 'Cc11_g10150' => 'ccan', 'CDE02G0299' => 'cde', 'CDE05G0590' => 'cde', 'CDE05G2772' => 'cde', 'CDE05G2786' => 'cde', 'CDE11G0129' => 'cde', 'Cfa007305' => 'cfa', 'Cfa018596' => 'cfa', 'Cfa021917' => 'cfa', 'Ciclev10015173m.g' => 'ccl', 'Ciclev10015864m.g' => 'ccl', 'Ciclev10020440m.g' => 'ccl', 'Ciclev10029146m.g' => 'ccl', 'CiPaw.03G048100' => 'cil', 'CiPaw.04G031600' => 'cil', 'CiPaw.13G071100' => 'cil', 'CiPaw.14G054900' => 'cil', 'CiPaw.15G085100' => 'cil', 'CiPaw.15G130300' => 'cil', 'CiPaw.16G085800' => 'cil', 'ClCG03G000330' => 'cla', 'ClCG05G022710' => 'cla', 'ClCG06G014850' => 'cla', 'ClCG08G005350' => 'cla', 'ClCG09G019520' => 'cla', 'COL.COLO4_05971' => 'col', 'COL.COLO4_11133' => 'col', 'COL.COLO4_20602' => 'col', 'COL.COLO4_29226' => 'col', 'Cpa.g.sc19.26' => 'cpa', 'Cpa.g.sc2.373' => 'cpa', 'Cpa.g.sc3.516' => 'cpa', 'Cpa.g.sc862.1' => 'cpa', 'Cre15.g635100' => 'cre', 'CsaV3_1G003800' => 'csa', 'CsaV3_1G036580' => 'csa', 'CsaV3_5G026860' => 'csa', 'CsaV3_5G034320' => 'csa', 'CsaV3_6G003540' => 'csa', 'CSS0000704' => 'camsi', 'CSS0017546' => 'camsi', 'CSS0030241' => 'camsi', 'CSS0038569' => 'camsi', 'CSS0045449' => 'camsi', 'CSS0046170' => 'camsi', 'DCAR_011276' => 'dca', 'DCAR_011541' => 'dca', 'DCAR_015140' => 'dca', 'DCAR_023659' => 'dca', 'DCAR_030155' => 'dca', 'Dinv09664' => 'din', 'Dinv09797' => 'din', 'Dinv10699' => 'din', 'Dinv21086' => 'din', 'Dinv25710' => 'din', 'Dinv28098' => 'din', 'Dinv28689' => 'din', 'Duzib068G1015' => 'dzi', 'Duzib084G0515' => 'dzi', 'Duzib147G1069' => 'dzi', 'Duzib168G0679' => 'dzi', 'Duzib170G0177' => 'dzi', 'Duzib187G1470' => 'dzi', 'Duzib205G0636' => 'dzi', 'Duzib248G1208' => 'dzi', 'Duzib251G0361' => 'dzi', 'ECA233G1916' => 'eca', 'ECA236G3356' => 'eca', 'ECA246G0068' => 'eca', 'ECA246G3575' => 'eca', 'ECA247G0457' => 'eca', 'EL10Ac6g14404' => 'bvu', 'EL10Ac7g15907' => 'bvu', 'Eucgr.B00721' => 'egr', 'Eucgr.G02322' => 'egr', 'Eucgr.I01705' => 'egr', 'FAN02G3931' => 'fan', 'FAN04G2513' => 'fan', 'FAN05G0553' => 'fan', 'FAN07G0493' => 'fan', 'FAN08G2620' => 'fan', 'FAN09G1933' => 'fan', 'FAN11G0094' => 'fan', 'FAN12G1023' => 'fan', 'FAN12G3480' => 'fan', 'FAN13G0527' => 'fan', 'FAN14G1087' => 'fan', 'FAN14G4037' => 'fan', 'FAN16G2757' => 'fan', 'FAN18G2509' => 'fan', 'FAN18G3399' => 'fan', 'FAN21G3719' => 'fan', 'FAN22G1861' => 'fan', 'FAN25G3168' => 'fan', 'FvH4_3g39550' => 'fve', 'FvH4_4g27390' => 'fve', 'FvH4_5g12150' => 'fve', 'FvH4_6g52200' => 'fve', 'Glyma.02G230800' => 'gma', 'Glyma.05G233700' => 'gma', 'Glyma.07G091400' => 'gma', 'Glyma.08G041100' => 'gma', 'Glyma.09G184600' => 'gma', 'Glyma.10G274300' => 'gma', 'Glyma.14G197900' => 'gma', 'Glyma.15G241200' => 'gma', 'Glyma.16G067000' => 'gma', 'Glyma.19G079600' => 'gma', 'Glyma.20G115600' => 'gma', 'Gohir.A01G185300' => 'ghi', 'Gohir.A05G108600' => 'ghi', 'Gohir.A08G094500' => 'ghi', 'Gohir.A09G031400' => 'ghi', 'Gohir.A09G047500' => 'ghi', 'Gohir.D01G176000' => 'ghi', 'Gohir.D05G108700' => 'ghi', 'Gohir.D08G105900' => 'ghi', 'Gohir.D09G031500' => 'ghi', 'Gohir.D09G048500' => 'ghi', 'Gorai.002G218400' => 'gra', 'Gorai.004G113000' => 'gra', 'Gorai.006G036400' => 'gra', 'Gorai.006G061600' => 'gra', 'Gorai.009G113000' => 'gra', 'GSVIVG01003983001' => 'vvi', 'GSVIVG01011897001' => 'vvi', 'GSVIVG01024661001' => 'vvi', 'HanXRQChr04g0100211' => 'han', 'HanXRQChr04g0121971' => 'han', 'HanXRQChr06g0169231' => 'han', 'HanXRQChr08g0213841' => 'han', 'HanXRQChr08g0228701' => 'han', 'HanXRQChr15g0474581' => 'han', 'HanXRQChr17g0549411' => 'han', 'HanXRQChr17g0552071' => 'han', 'Haze_14788' => 'cav', 'Haze_17481' => 'cav', 'Haze_18671' => 'cav', 'Haze_22025' => 'cav', 'Haze_24398' => 'cav', 'Hma1.2p1_0061F.1_g033920' => 'hma', 'Hma1.2p1_0279F.1_g112020' => 'hma', 'Hma1.2p1_0592F.1_g185370' => 'hma', 'Hma1.2p1_0841F.1_g226950' => 'hma', 'Hma1.2p1_2942F.1_g330630' => 'hma', 'HPP92_006141' => 'vpl', 'HPP92_010396' => 'vpl', 'HPP92_016583' => 'vpl', 'Hund13018' => 'sun', 'Hund18955' => 'sun', 'Hund20692' => 'sun', 'Hund20806' => 'sun', 'Hund25064' => 'sun', 'Lalb_Chr02g0146001' => 'lal', 'Lalb_Chr05g0222511' => 'lal', 'Lalb_Chr09g0331091' => 'lal', 'Lalb_Chr14g0362941' => 'lal', 'Lalb_Chr16g0387811' => 'lal', 'Lalb_Chr17g0342141' => 'lal', 'Lalb_Chr17g0345351' => 'lal', 'Lalb_Chr21g0308941' => 'lal', 'Lalb_Chr22g0360591' => 'lal', 'Lj1g0026201' => 'lja', 'Lj2g0004218' => 'lja', 'Lj3A1014G44' => 'lonja', 'Lj4g0020741' => 'lja', 'Lj5C148T4' => 'lonja', 'Lj5g0019912' => 'lja', 'Lj6A759T75' => 'lonja', 'Lj9A426T60' => 'lonja', 'LjContig00141g0007684' => 'lja', 'Lju41C44G13' => 'lonja', 'Lju41E44T3' => 'lonja', 'Lsat_1_v5_gn_0_5521' => 'lsa', 'Lsat_1_v5_gn_0_5541' => 'lsa', 'Lsat_1_v5_gn_3_59241' => 'lsa', 'Lsat_1_v5_gn_7_6501' => 'lsa', 'Lsat_1_v5_gn_9_18261' => 'lsa', 'Manes.01G012000' => 'mes', 'Manes.02G216600' => 'mes', 'Manes.05G137600' => 'mes', 'Manes.06G068600' => 'mes', 'Manes.14G102400' => 'mes', 'Manes.15G154300' => 'mes', 'Manes.18G141029' => 'mes', 'Mapoly0049s0067' => 'mpo', 'Mapoly0122s0029' => 'mpo', 'MBI03_g33618_MAGBIO' => 'mbi', 'MBI08_g04807_MAGBIO' => 'mbi', 'MBI13_g09690_MAGBIO' => 'mbi', 'MCO10G106' => 'mco', 'MD03G1059900' => 'mdo', 'MD06G1215800' => 'mdo', 'MD09G1019800' => 'mdo', 'MD11G1063100' => 'mdo', 'MD13G1042200' => 'mdo', 'MD14G1226400' => 'mdo', 'MD16G1043000' => 'mdo', 'MD17G1020400' => 'mdo', 'Medtr1g110870' => 'mtr', 'Medtr5g072780' => 'mtr', 'Medtr7g032240' => 'mtr', 'Medtr8g104190' => 'mtr', 'MELO3C011576.2' => 'cme', 'MELO3C012248.2' => 'cme', 'MELO3C017304.2' => 'cme', 'MELO3C021608.2' => 'cme', 'MELO3C035273.2' => 'cme', 'Migut.E00340' => 'egut', 'Migut.I00345' => 'egut', 'Migut.K01424' => 'egut', 'Migut.L01064' => 'egut', 'MSTRG.13531' => 'ama', 'MSTRG.2236' => 'ama', 'MSTRG.24053' => 'ama', 'MSTRG.838' => 'ama', 'Nitab4.5_0000057g0280' => 'nta', 'Nitab4.5_0000874g0020' => 'nta', 'Nitab4.5_0000935g0190' => 'nta', 'Nitab4.5_0000974g0020' => 'nta', 'Nitab4.5_0001031g0320' => 'nta', 'Nitab4.5_0003373g0100' => 'nta', 'Nitab4.5_0008741g0010' => 'nta', 'Nitab4.5_0009734g0010' => 'nta', 'Nn2g13239' => 'nnu', 'Nn3g17837' => 'nnu', 'Nn3g20358' => 'nnu', 'Nn4g22505' => 'nnu', 'Nn4g23831' => 'nnu', 'Oeu034246.1' => 'oeu', 'Oeu038068.1' => 'oeu', 'Oeu039281.1' => 'oeu', 'Oeu050163.1' => 'oeu', 'Oeu050450.1' => 'oeu', 'Oeu054650.1' => 'oeu', 'Os02g0731700' => 'osa', 'Os03g0711100' => 'osa', 'Os06g0264200' => 'osa', 'Os08g0119700' => 'osa', 'Peaxi162Scf00015g00927' => 'pax', 'Peaxi162Scf00382g00067' => 'pax', 'Peaxi162Scf00420g00155' => 'pax', 'Peaxi162Scf01346g00018' => 'pax', 'PGR004G0565' => 'pgr', 'PGR083G2831' => 'pgr', 'PGR119G0346' => 'pgr', 'PGR142G0166' => 'pgr', 'PGSC0003DMG400005633' => 'stu', 'PGSC0003DMG400007749' => 'stu', 'PGSC0003DMG400012618' => 'stu', 'PGSC0003DMG400014566' => 'stu', 'Phvul.002G316100' => 'pvu', 'Phvul.003G036000' => 'pvu', 'Phvul.004G157300' => 'pvu', 'Phvul.007G027200' => 'pvu', 'Phvul.008G147400' => 'pvu', 'Phvul.008G257300' => 'pvu', 'Potri.001G281700' => 'ptr', 'Potri.001G339200' => 'ptr', 'Potri.008G120400' => 'ptr', 'Potri.009G077100' => 'ptr', 'Potri.010G125100' => 'ptr', 'Potri.015G054600' => 'ptr', 'Pp3c10_22950' => 'ppa', 'Pp3c12_21300' => 'ppa', 'Pp3c14_8140' => 'ppa', 'Pp3c18_13350' => 'ppa', 'Pp3c19_2450' => 'ppa', 'Pp3c1_950' => 'ppa', 'Pp3c22_5440' => 'ppa', 'Pp3c2_35540' => 'ppa', 'Pp3c3_35020' => 'ppa', 'Pp3c4_7080' => 'ppa', 'Pp3c7_23900' => 'ppa', 'Pp3c8_1870' => 'ppa', 'Prupe.1G310900' => 'ppe', 'Prupe.3G296700' => 'ppe', 'Prupe.5G221000' => 'ppe', 'Prupe.6G050300' => 'ppe', 'Psat2g054040' => 'psa', 'Psat6g228360' => 'psa', 'Psat7g011960' => 'psa', 'Psat7g037680' => 'psa', 'PSO017G0608' => 'pso', 'PSO017G6340' => 'pso', 'PSO339G5110' => 'pso', 'PSO478G1753' => 'pso', 'PSO478G1997' => 'pso', 'PSO801G0748' => 'pso', 'QL01p040049' => 'qlo', 'QL01p042619' => 'qlo', 'QL02p073497' => 'qlo', 'QL10p025240' => 'qlo', 'RcHm_v2.0_Chr2g0173701' => 'rch', 'RcHm_v2.0_Chr4g0435191' => 'rch', 'RcHm_v2.0_Chr5g0071321' => 'rch', 'RcHm_v2.0_Chr7g0185411' => 'rch', 'Rhsim01G0240200' => 'rsi', 'Rhsim09G0108100' => 'rsi', 'Rhsim10G0013100' => 'rsi', 'Rhsim12G0084500' => 'rsi', 'Rhsim12G0143500' => 'rsi', 'RhsimUnG0005000' => 'rsi', 'Sabra08G0091400' => 'sbr', 'Sabra10G0095000' => 'sbr', 'Sabra15G0073600' => 'sbr', 'Sabra15G0074800' => 'sbr', 'Sabra16G0175200' => 'sbr', 'SalBow5G0828' => 'sbo', 'SalBow7G4716' => 'sbo', 'SalBow8G1399' => 'sbo', 'SalBow8G2735' => 'sbo', 'Sc07g0004320' => 'sci', 'Sc11g0003380' => 'sci', 'Sed0001095' => 'sed', 'Sed0007705' => 'sed', 'Sed0008506' => 'sed', 'Sed0013896' => 'sed', 'Sed0020394' => 'sed', 'Sed0023618' => 'sed', 'SEGI_19043' => 'sgi', 'SEGI_19746' => 'sgi', 'SEGI_33443' => 'sgi', 'SGA_v2.0_scaffold124G33527' => 'sas', 'SGA_v2.0_scaffold21G09388' => 'sas', 'SGA_v2.0_scaffold47G17530' => 'sas', 'SMO356G0270' => 'smo', 'SMO361G0452' => 'smo', 'SMO361G0475' => 'smo', 'SMO364G0443' => 'smo', 'Solyc02g093590.3' => 'sly', 'Solyc03g119540.3' => 'sly', 'Solyc04g007210.3' => 'sly', 'Solyc05g009310.3' => 'sly', 'Sopen02g038060' => 'spe', 'Sopen03g038370' => 'spe', 'Sopen04g002270' => 'spe', 'Sopen05g005060' => 'spe', 'Sp1g05770' => 'spa', 'Sp1g22770' => 'spa', 'Sp1g36020' => 'spa', 'Sp5g23590' => 'spa', 'Sp6g29650' => 'spa', 'TAR371G0621' => 'tar', 'TAR371G1296' => 'tar', 'TAR374G0409' => 'tar', 'TAR622G0070' => 'tar', 'TAR622G0145' => 'tar', 'TAR633G2024' => 'tar', 'TAR636G0084' => 'tar', 'THA.LOC104798712' => 'tha', 'THA.LOC104804873' => 'tha', 'THA.LOC104816131' => 'tha', 'THA.LOC104818543' => 'tha', 'THA.LOC104821935' => 'tha', 'THA.LOC104826278' => 'tha', 'Thecc.02G231000' => 'tca', 'Thecc.03G034600' => 'tca', 'Thecc.04G023900' => 'tca', 'Thecc.09G356100' => 'tca', 'Thhalv10007685m.g' => 'esa', 'Thhalv10008808m.g' => 'esa', 'Thhalv10011633m.g' => 'esa', 'Thhalv10014044m.g' => 'esa', 'Thhalv10018663m.g' => 'esa', 'TPR.G1087' => 'tpr', 'TPR.G1493' => 'tpr', 'TPR.G29711' => 'tpr', 'TPR.G32690' => 'tpr', 'TWI12G0090' => 'twi', 'TWI31G0677' => 'twi', 'TWI56G1198' => 'twi', 'TWI60G1239' => 'twi', 'TWI79G1152' => 'twi', 'TWI79G1170' => 'twi', 'unitig_22.g6870' => 'ugi', 'unitig_26.g10259' => 'ugi', 'unitig_27.g25190' => 'ugi', 'unitig_52.g17135' => 'ugi', 'unitig_748.g8691' => 'ugi', 'unitig_8.g3442' => 'ugi', 'vmacro01382' => 'vma', 'vmacro05900' => 'vma', 'vmacro16449' => 'vma', 'VMungo0251G2136' => 'vmu', 'VMungo0464G1761' => 'vmu', 'VMungo0647G1603' => 'vmu', 'VMungo0720G0433' => 'vmu', 'VMungo1215G0958' => 'vmu', 'VMungo1383G1671' => 'vmu', 'Zm00001eb054810' => 'zma', 'Zm00001eb173520' => 'zma', 'Zm00001eb216410' => 'zma', 'Zm00001eb253650' => 'zma', 'Zm00001eb261240' => 'zma', 'Zm00001eb280600' => 'zma', 'Zm00001eb379950' => 'zma' ) $gf_id = 'HOM05D001106' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001106' ) $data_identifier = 'HOM05D001106' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 6, 'cqu' => (int) 4, 'bca' => (int) 30, 'bol' => (int) 14, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 5, 'lal' => (int) 9, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 12, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379950' $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